I think I'm missing something - why not just use a $25 trickle charger from Sears or somewhere ?
If you really want something cool and different then a retractable roof during daylight hours would be really cool and best vs. a skylight. Some glass limits the output of solar panels due to decreased photometric transmission and my not charge your battery even with the skylight.
Placing solar panels behind windows will cost you quite a bit of energy...
From the iron content of standard glass (which blocks some light), to Low-E glass which blocks some more light, to the extra reflections from additional air/glass interfaces--you will lose a lot of power (50% or more????).
Here is an example of how
glass interferes with a solar cell's spectral response.
The simple test... Take any silicon solar panel (big or small) and connect it to a DVM set amps. The amp reading in sun and behind glass will give you a very exact reading on how much power you will lose (the current output of a shorted silicon solar panel is proportional to the amount of sunlight energy hitting the panel).
You also need to take into account that fact that most people's windows are near 90 degrees (vertical). And for much of North America, the ideal angles are closer to 20-40 degrees. Only in winter (and farther towards the north) does running a panel vertical not hurt you (and in some cases may help increase power collected during the winter months).
I would play it safe and buy one from Sears or somewhere.
http://www.sears.com/diehard-batter...p-02871219000P?prdNo=1&blockNo=1&blockType=G1